degnorm {DegNorm} | R Documentation

## Main function to perform degradation normalization.

### Description

`degnorm` calcualtes the degradation index score for each gene within each sample and return the degradation-normalized read counts.

### Usage

    degnorm(read_coverage,counts,iteration,loop,down_sampling=1,grid_size=10,
    cores=1)

### Arguments

`read_coverage` | a list of converage matrices, one per gene
`counts` | dataframe of read counts, each row for one gene, and column for sample. The order and number of genes must match the order in read_coverage matrices.
`iteration` | iteration number for degnorm algorithm. 5 is sufficient.
`loop` | iteration number inside of nonnegative matrix factorization-over approximation. Default is 100.
`down_sampling` | 1 for yes (default) and 0 for no. If yes, average coverage score is calcualted on a grid of size specified by grid_size argument. The new coverage matrix formed by the grid average score will be used for baseline selection. This increases the efficiency of algorithm while maintaining comparable accuracy.
`grid_size` | default size is 10 bp.
`cores` | number of cores. Default number if 1. Users should input the maximum possible number of cores for efficiency.

### Value

`degnorm` outputs a list of following objects:

`counts` | a data.drame of read counts for each gene within each sample.
`counts_normed` | a data.drame of degradation-normalized read counts for each gene within each sample.
`DI` | a matrix of degradation index scores for each gene within each sample.
`K` | normalizing scale factor for each gene within each sample after accounting for degradation normalization.
`convergence` | convergence tag; 0 = degnorm was not done on this gene because smaller counts or too short length.1 = degnorm was done with baseline selection. 2 = degnorm done without baseline selection because gene length (after filtering out low count regions)<200 bp. 3= baseline was found, but DI score is too large. 4 = baseline selection didn't coverge.
`envelop` | list of the envelop curves for all genes.

### Examples

    ##coverage_res_chr21 is a \code{CoverageClass} object from DegNorm Package.
    data(coverage_res_chr21)
    res_DegNorm = degnorm(read_coverage = coverage_res_chr21[[1]],
                        counts = coverage_res_chr21[[2]],
                        iteration = 2,
                        down_sampling = 1,
                        grid_size=10,
                        loop = 20,
                        cores=2)

[Package DegNorm version 1.0.0 Index]